Cannot find "umap" in Seurat object

[Lux91]

Hi,
I'm currently testing your method on my scRNA-Seq datasets with Seurat, I'm using the 2 scripts you included in the examples directory, I just have one issue (see the name of this thread) when running the "2_seurat_further_visualisations.R" script since at some point you put the following code (around row 88 of the script):
plot <- DimPlot( obj, reduction = "umap", group.by = glue::glue("{reduction}.{assay}_res.{choice}"), pt.size = 0.5, )
but in the first script (1_seurat_pipeline.R), you never computed the UMAP dimensionality reduction (running the RunUMAP function). I checked both the "pipeline.R" and "helper_functions.R" scripts and it appears you never included it, is there a correct part where you intended it to be for the whole method to work correctly?
Thanks in advance for your help :)

[MenonLab]

Hi there,
This is a good point - since the standard example pipeline searches over the "resolution" parameter (and not the number of PCs), the assumption is that UMAP calculation has already been done on the object before the pipeline is run. tThe UMAP coordinates are independent of the choice of resolution parameter, so they only needs to be calculated once.

Also, we have forked an updated version of chooseR with some bug fixes here:
https://github.com/menonlab/chooseR
We will continue to post updates there as well.

Vilas